While a firm date has not been announced, as early as March 2013, the Golden Gate Bridge will switch to "All Electronic" toll collection.

First off, only going Southbound on the Golden Gate Bridge will create a toll charge.

And unless you pay for the Toll before you cross, your rental car company can charge fees and penalities.  Doing it as part of the rental car agreement will reduce the amounts of the additional costs, which will be automatically added to your credit/debit card as an additional amount.

The official Golden Gate Bridge website has a detailed list of the fees and rules for each participating Vehicle Rental Company.

http://www.goldengate.org/tolls/renta...

If you are traveling in the area, be prepared for this change, or do some further research to see if the system has been converted.